Complex text alignment in bash

If all your commands and arguments do not contain #, and one other character (say the ASCII character given by byte 1), you can insert that other character as an extra separator and use column to align the comments (see this answer). So, something like:

$ sed $'s/#/\001#/' input-file | column -ets $'\001'
# Lines starting with # stay the same
# Empty lines stay the same
# only lines with comments should change

ls                                        # show all major directories
                                          # and other things

cd                                        # The cd command - change directory
                                          # will allow the user to change between file directories

touch                                     # The touch command, the make file command
                                          # allows users to make files using the Linux CLI #  example, cd ~

bar foo baz                               # foo foo foo

If your column doesn't support -e to avoid eliminating empty lines, you could add something to empty lines (for example, a space, or the separator character used above):

$ sed $'s/#/\001#/;s/^$/\001/' input-file | column -ts $'\001'
# Lines starting with # stay the same
# Empty lines stay the same
# only lines with comments should change

ls                                        # show all major directories
                                          # and other things

cd                                        # The cd command - change directory
                                          # will allow the user to change between file directories

touch                                     # The touch command, the make file command
                                          # allows users to make files using the Linux CLI #  example, cd ~

bar foo baz                               # foo foo foo

Text processing with the shell alone is a bit awkward and may be error prone (see "Why is using a shell loop to process text considered bad practice?"). It's generally better to use and other programming language for tasks such as these.

---

perl -ne 'if (/^([^#]+?)\s*#(.*)$/) { printf("%-16s#%s\n", $1, $2) } else { print }' file

This uses Perl to capture the bit in front of the # (discarding spaces between the last word and the #) and the bit after. If the match was successful, it allocates 16 character locations for the text and prints the formatted text and comment. If the match was not successful (because the line was blank or started with an #), the line is printed without modification.

# Lines starting with # stay the same
# Empty lines stay the same
# only lines with comments should change

ls              # show all major directories
                # and other things

cd              # The cd command - change directory
                # will allow the user to change between file directories

touch           # The touch command, the make file command
                # allows users to make files using the Linux CLI #  example, cd ~

bar foo baz     # foo foo foo

Here's a Python script that should do what you want:

#!/usr/bin/env python
# -*- encoding: ascii -*-
"""align.py"""

import re
import sys

# Read the data from the file into a list
lines = []
with open(sys.argv[1], 'r') as textfile:
    lines = textfile.readlines()

# Iterate through the data once to get the maximum indentation
max_indentation = 0
comment_block = False
for line in lines:

    # Check for the end of a comment block
    if comment_block:
        if not re.match(r'^\s*#.*$', line):
            comment_block = False

    # Check for the beginning of a comment block
    else:
        if re.match(r'^[^#]*[^ #].*#.*$', line):
            comment_block = True
            indentation = line.index('#')
            max_indentation = max(max_indentation, indentation)

# Iterate through the data a second time and output the reformatted text
comment_block = False
for line in lines:
    if comment_block:
        if re.match(r'^\s*#.*$', line):
            line = ' ' * max_indentation + line.lstrip()
        else:
            comment_block = False
    else:
        if re.match(r'^[^#]*[^ #].*#.*$', line):
            pre, sep, suf = line.partition('#')
            line = pre.ljust(max_indentation) + sep + suf
            comment_block = True

    sys.stdout.write(line)

Run it like so:

python align.py input.txt

It produces the following output:

# Lines starting with # stay the same
# Empty lines stay the same
# only lines with comments should change

ls                # show all major directories
                  # and other things

cd                # The cd command - change directory  
                  # will allow the user to change between file directories

touch             # The touch command, the make file command 
                  # allows users to make files using the Linux CLI #  example, cd ~

bar foo baz       # foo foo foo